Public Member Functions
public void	run ()

Detailed Description

Description

A parser class to parse the VGNC source.
VGNC is the official naming source for some vertebrates species

-data_uri = https://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
-file_format = TSV
-columns = [
    taxon_id
    vgnc_id
    symbol
    name
    locus_group
    locus_type
    status
    location
    location_sortable:
    alias_symbol
    alias_name
    prev_symbol
    prev_name
    gene_family
    gene_family_id
    date_approved_reserved
    date_symbol_changed
    date_name_changed
    date_modified
    entrez_id
    ensembl_gene_id
    uniprot_ids
  ]

Only columns listed in \@required_columns are mandatory.

Synopsis

my $parser = XrefParser::VGNCParser->new($db->dbh);
 
my $parser->run( {
  source_id  => 144,
  species_id => 9598,
  files      => ['VGNC/vgnc_gene_set_All.txt.gz'],
} );

Definition at line 51 of file VGNCParser.pm.

Member Function Documentation

◆ run()

public void XrefParser::VGNCParser::run ( )

  Description: Runs the VGNCParser
  Return type: none
  Exceptions : throws on all processing errors
  Caller     : ParseSource in the xref pipeline

Code:

click to view

sub run {
  my ($self, $ref_arg) = @_;
 
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $files        = $ref_arg->{files};
  my $verbose      = $ref_arg->{verbose} // 0;
  my $dbi          = $ref_arg->{dbi} // $self->dbi;
 
 
  if ( (!defined $source_id) || (!defined $species_id) || (!defined $files) ) {
    confess "Need to pass source_id, species_id and files as pairs";
  }
 
  my $file = @{$files}[0];
 
  my $count = 0;
 
  my $file_io = $self->get_filehandle($file);
 
  if ( !defined $file_io ) {
    confess "Can't open VGNC file '$file'\n";
  }
 
  my $source_name = $self->get_source_name_for_source_id($source_id, $dbi);
 
  # Create a hash of all valid taxon_ids for this species
  my %species2tax = $self->species_id2taxonomy($dbi);
  push @{$species2tax{$species_id}}, $species_id;
  my @tax_ids = @{$species2tax{$species_id}};
  my %taxonomy2species_id = map{ $_=>$species_id } @tax_ids;
 
  my $input_file = Text::CSV->new({
    sep_char       => "\t",
    empty_is_undef => 1,
    binary => 1
  }) or confess "Cannot use file '$file': ".Text::CSV->error_diag();
 
  # header must contain these columns
  my @required_columns = qw(
    taxon_id
    ensembl_gene_id
    vgnc_id
    symbol
    name
    alias_symbol
    prev_symbol
  );
 
  # get header columns
  my @columns = @{ $input_file->getline( $file_io ) };
 
  # die if some required_column is not in columns
  foreach my $colname (@required_columns) {
    if ( !grep { /$colname/xms } @columns ) {
      confess "Can't find required column '$colname' in VGNC file '$file'\n";
    }
  }
 
  $input_file->column_names( @columns );
 
  while ( my $data = $input_file->getline_hr( $file_io ) ) {
 
    # skip data for other species
    next if ( !exists $taxonomy2species_id{$data->{'taxon_id'}} );
 
    if ( $data->{'ensembl_gene_id'} ) {              # Ensembl direct xref
      $self->add_to_direct_xrefs({
        stable_id  => $data->{'ensembl_gene_id'},
        type       => 'gene',
        acc        => $data->{'vgnc_id'},
        label      => $data->{'symbol'},
        desc       => $data->{'name'},
        dbi        => $dbi,
        source_id  => $source_id,
        species_id => $species_id
      });
 
      $self->add_synonyms_for_hgnc({
        source_id  => $source_id,
        name       => $data->{'vgnc_id'},
        species_id => $species_id,
        dbi        => $dbi,
        dead       => $data->{'alias_symbol'},
        alias      => $data->{'prev_symbol'}
      });
 
      $count++;
    }
 
  }
 
  $input_file->eof or confess "Error parsing file '$file': " . $input_file->error_diag();
  $file_io->close();
 
  if($verbose){
    print "Loaded a total of $count VGNC xrefs\n";
  }
 
  return 0; # successful
}

The documentation for this class was generated from the following file:

ensembl/misc-scripts/xref_mapping/XrefParser/VGNCParser.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ run()